Self-Attraction Removal from Oritatami Systems

Abstract

RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene by an RNA polymerase. Oritatami is a computational model of this phenomenon, which lets its sequence of beads (abstract molecules) taken from a finite alphabet [Formula: see text] fold cotranscriptionally via interactions between beads according to its rule set. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. Self-attraction is one of the major challenges in the construction of intrinsic oritatami systems, which can simulate even the dynamics of all the oritatami systems.